Some code to look at the overall phylogenetic placement of the taxa we are modeling.

Previous literature has identified that overall trends in phenology are thought to be shared across the phylogeny for plants (i.e. evolutionary history will influence flowering). We can both: 1) Test this hypothesis in my datasets. 2) Evaluate the overall scope of the tree that we are capturing in this analysis.

Load in Packages

library(rotl) # calls the open tree api to give us a rough idea of the current phylogeny, I would still take these with a grain of salt but its not a bad exploratory option
library(data.table)
library(ggplot2)
library(stringr)
library(tidyverse)
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library(phytools)
## Loading required package: ape
## 
## Attaching package: 'ape'
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## 
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## Loading required package: maps
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library(ape)

Load Data

Simplify to just names and create a simple subset for illustration purposes

Grab a tree for these tips

Labeling Phylogeny

In order to address both (1) and (2), it may be helpful to label the phylogeny as a overall visual.

Create some labeled plots

New plan, new plan: Find representative taxa 1) That have the best amount of temporal coverage for year by year phenometric measurements

named_data_labeled <- fread("/home/jt-miller/Gurlab/sliding-phenology/data/processed/blooming-period-dataset.csv") 
# 
flowering_data <- named_data_labeled


result_table <- flowering_data %>%
  group_by(speciesName, year) %>%
  summarise(
    condition_satisfied = n() > 5 & n_distinct(doy) >= 3
  ) %>%
  group_by(speciesName) %>%
  summarise(
    num_years_condition_satisfied = sum(condition_satisfied)
  )
## `summarise()` has grouped output by 'speciesName'. You can override using the
## `.groups` argument.
flowering_data2 <- merge(flowering_data, result_table, by = "speciesName")
flowering_data3 <- flowering_data2 %>% 
filter(!bloom_period == "unknown") %>%  # doesnt contribute to known phenology
  group_by(speciesName) %>%
  mutate(bloomSpecificity = case_when(
    n_distinct(bloom_period) == 1 & bloom_period == 'spring bloomer' ~ "spring bloomer",
    n_distinct(bloom_period) == 1 & bloom_period == 'fall bloomer' ~ "fall bloomer",
     n_distinct(bloom_period) > 1 ~ "opportunistic bloomer"
  )) %>% 
  distinct(speciesName, bloomSpecificity, .keep_all = TRUE)

flowering_data4 <- flowering_data3 %>% 
  filter(num_years_condition_satisfied >= 25)

name_subset <- flowering_data3$speciesName

resolved_subset <- tnrs_match_names(name_subset)
## Warning: , Acmispon rigidus, Malacothamnus enigmaticus, Ottleya strigosa,
## Simpsonanthus jonesii are not matched
# resolved_subset2 <- filter(resolved_subset, !ott_id == 5502771)
# resolved_subset2 <- filter(resolved_subset2, !ott_id == 173589)
# tree_object <- tol_induced_subtree(ott_ids = ott_id(resolved_subset2)) # appends lineages from open tree

in_tree <- is_in_tree(ott_id(resolved_subset))
in_tree
##                    Abronia villosa                  Senegalia greggii 
##                               TRUE                               TRUE 
##               Acalypha californica      Acamptopappus sphaerocephalus 
##                               TRUE                               TRUE 
##               Achyronychia cooperi                Acmispon americanus 
##                               TRUE                               TRUE 
##               Acmispon argophyllus                    Acmispon glaber 
##                               TRUE                               TRUE 
##                Acmispon heermannii                 Lotus salsuginosus 
##                               TRUE                               TRUE 
##                Acmispon micranthus                 Acmispon strigosus 
##                               TRUE                               TRUE 
##        Adenophyllum porophylloides                      Agave deserti 
##                               TRUE                               TRUE 
##                Aliciella latifolia                 Allionia incarnata 
##                               TRUE                               TRUE 
##                  Allium fimbriatum                   Allium monticola 
##                               TRUE                               TRUE 
##                 Allium peninsulare              Amaranthus fimbriatus 
##                               TRUE                               TRUE 
##              Ambrosia acanthicarpa                    Ambrosia dumosa 
##                               TRUE                               TRUE 
##                   Ambrosia salsola               Amsinckia intermedia 
##                               TRUE                               TRUE 
##                Amsinckia menziesii               Amsinckia tessellata 
##                               TRUE                               TRUE 
##                Antirrhinum filipes                   Aphyllon cooperi 
##                               TRUE                               TRUE 
##              Arctostaphylos glauca                    Argemone munita 
##                               TRUE                               TRUE 
##              Aristida adscensionis                  Aristida purpurea 
##                               TRUE                               TRUE 
##              Artemisia ludoviciana                 Asclepias albicans 
##                               TRUE                               TRUE 
##                 Asclepias subulata                  Astragalus aridus 
##                               TRUE                               TRUE 
##               Astragalus coccineus             Astragalus crotalariae 
##                               TRUE                               TRUE 
##            Astragalus didymocarpus               Astragalus douglasii 
##                               TRUE                               TRUE 
##            Astragalus lentiginosus            Astragalus nuttallianus 
##                               TRUE                               TRUE 
##                 Astragalus palmeri            Astragalus tricarinatus 
##                               TRUE                               TRUE 
##           Atrichoseris platyphylla                 Atriplex canescens 
##                               TRUE                               TRUE 
##               Atriplex hymenelytra                 Atriplex polycarpa 
##                               TRUE                               TRUE 
##                    Ayenia compacta             Baccharis brachyphylla 
##                               TRUE                               TRUE 
##              Baccharis salicifolia                 Bahiopsis parishii 
##                               TRUE                               TRUE 
##               Baileya multiradiata               Baileya pauciradiata 
##                               TRUE                               TRUE 
##                      Bebbia juncea                   Bernardia incana 
##                               TRUE                               TRUE 
##                Boechera johnstonii                 Boerhavia coccinea 
##                               TRUE                               TRUE 
##                 Boerhavia coulteri                Boerhavia triquetra 
##                               TRUE                               TRUE 
##                 Boerhavia wrightii             Bouteloua aristidoides 
##                               TRUE                               TRUE 
##                  Bouteloua barbata              Echinopepon bigelovii 
##                               TRUE                               TRUE 
##              Brassica tournefortii           Brickellia atractyloides 
##                               TRUE                               TRUE 
##              Brickellia frutescens                 Bromus berteroanus 
##                               TRUE                               TRUE 
##                 Bromus madritensis                    Bromus tectorum 
##                               TRUE                               TRUE 
##         Hoffmannseggia microphylla                  Cistanthe ambigua 
##                               TRUE                               TRUE 
## Calandrinia ciliata var. menziesii               Calochortus concolor 
##                               TRUE                               TRUE 
##                 Calochortus dunnii                Calochortus palmeri 
##                               TRUE                               TRUE 
##                 Calycoseris parryi               Calycoseris wrightii 
##                               TRUE                               TRUE 
##             Calyptridium monandrum                Camissonia brevipes 
##                               TRUE                              FALSE 
##               Eulobus californicus            Camissonia cardiophylla 
##                               TRUE                              FALSE 
##              Chylismia claviformis                 Camissonia pallida 
##                               TRUE                              FALSE 
##                Eremothera refracta            Camissoniopsis bistorta 
##                               TRUE                               TRUE 
##             Camissoniopsis confusa             Camissoniopsis pallida 
##                               TRUE                               TRUE 
##                 Castilleja exserta               Castilleja foliolosa 
##                               TRUE                               TRUE 
##                   Castilleja minor               Streptanthus cooperi 
##                               TRUE                               TRUE 
##                  Caulanthus hallii            Caulanthus lasiophyllus 
##                               TRUE                               TRUE 
##                Caulanthus simulans               Ceanothus perplexans 
##                               TRUE                              FALSE 
##                  Cenchrus setaceus               Centaurea melitensis 
##                               TRUE                               TRUE 
##             Cercocarpus betuloides          Chaenactis artemisiifolia 
##                               TRUE                               TRUE 
##            Chaenactis carphoclinia               Chaenactis fremontii 
##                               TRUE                               TRUE 
##            Chaenactis glabriuscula              Chaenactis stevioides 
##                               TRUE                               TRUE 
##                Euphorbia polycarpa             Chenopodiastrum murale 
##                               TRUE                               TRUE 
##             Chenopodiastrum murale                 Chilopsis linearis 
##                               TRUE                               TRUE 
##             Chorizanthe brevicornu              Chorizanthe corrugata 
##                               TRUE                               TRUE 
##              Chorizanthe fimbriata                 Chorizanthe rigida 
##                               TRUE                               TRUE 
##                 Chylismia brevipes             Chylismia cardiophylla 
##                               TRUE                               TRUE 
##              Chylismia claviformis                  Cistanthe ambigua 
##                               TRUE                               TRUE 
##               Claytonia parviflora                  Cleomella arborea 
##                               TRUE                               TRUE 
##                  Cleomella arborea              Cleomella obtusifolia 
##                               TRUE                               TRUE 
##              Coleogyne ramosissima                      Condea emoryi 
##                               TRUE                               TRUE 
##         Corethrogyne filaginifolia                   Crassula connata 
##                               TRUE                               TRUE 
##               Crossosoma bigelovii                Croton californicus 
##                               TRUE                               TRUE 
##          Johnstonella angustifolia               Cryptantha barbigera 
##                               TRUE                               TRUE 
##             Johnstonella holoptera               Cryptantha decipiens 
##                               TRUE                               TRUE 
##                 Cryptantha ganderi              Cryptantha intermedia 
##                               TRUE                               TRUE 
##                Cryptantha maritima               Eremocarya micrantha 
##                               TRUE                               TRUE 
##                Cryptantha muricata              Cryptantha nevadensis 
##                               TRUE                               TRUE 
##              Cryptantha pterocarya                Cryptantha racemosa 
##                               TRUE                               TRUE 
##               Cryptantha utahensis                  Cucurbita palmata 
##                               TRUE                               TRUE 
##                Cuscuta californica            Cuscuta psorothamnensis 
##                               TRUE                               TRUE 
##           Cylindropuntia bigelovii         Cylindropuntia echinocarpa 
##                               TRUE                               TRUE 
##           Cylindropuntia fosbergii             Cylindropuntia ganderi 
##                               TRUE                               TRUE 
##         Cylindropuntia ramosissima                       Dalea mollis 
##                               TRUE                               TRUE 
##                   Dalea mollissima                    Datura discolor 
##                               TRUE                               TRUE 
##                    Datura wrightii                Delphinium parishii 
##                               TRUE                               TRUE 
##                 Dendromecon rigida                Descurainia pinnata 
##                               TRUE                               TRUE 
##                  Dicoria canescens              Dimorphotheca sinuata 
##                               TRUE                               TRUE 
##                 Diplacus bigelovii                 Diplacus calycinus 
##                               TRUE                               TRUE 
##            Dichelostemma capitatum                 Ditaxis lanceolata 
##                               TRUE                               TRUE 
##                    Ditaxis serrata                    Ditaxis serrata 
##                               TRUE                               TRUE 
##               Dithyrea californica               Tomostima cuneifolia 
##                               TRUE                               TRUE 
##               Dudleya pulverulenta                 Dudleya lanceolata 
##                               TRUE                               TRUE 
##                     Dudleya saxosa           Echinocereus engelmannii 
##                               TRUE                               TRUE 
##           Ehrendorferia chrysantha            Emmenanthe penduliflora 
##                               TRUE                               TRUE 
##                     Encelia actoni                   Encelia farinosa 
##                               TRUE                              FALSE 
##                 Encelia frutescens                     Ephedra aspera 
##                               TRUE                               TRUE 
##                    Epilobium canum                 Epipactis gigantea 
##                               TRUE                               TRUE 
##                   Eremalche exilis             Eremalche rotundifolia 
##                               TRUE                               TRUE 
##                  Eremocarya lepida               Eremocarya micrantha 
##                               TRUE                               TRUE 
##                 Eremothera boothii         Eremothera chamaenerioides 
##                               TRUE                               TRUE 
##                Eremothera refracta              Eriastrum densifolium 
##                               TRUE                               TRUE 
##                 Eriastrum diffusum                 Eriastrum eremicum 
##                               TRUE                               TRUE 
##             Ericameria brachylepis            Ericameria linearifolia 
##                               TRUE                               TRUE 
##              Ericameria paniculata                 Conyza bonariensis 
##                               TRUE                               TRUE 
##                Erigeron canadensis           Eriodictyon crassifolium 
##                               TRUE                               TRUE 
##            Eriodictyon trichocalyx                 Eriogonum deflexum 
##                               TRUE                               TRUE 
##                Eriogonum elongatum             Eriogonum fasciculatum 
##                               TRUE                               TRUE 
##                  Eriogonum gracile                 Eriogonum inflatum 
##                               TRUE                               TRUE 
##                 Eriogonum pusillum                Eriogonum reniforme 
##                               TRUE                               TRUE 
##                 Eriogonum thomasii                 Eriogonum thurberi 
##                               TRUE                               TRUE 
##                Eriogonum trichopes                 Eriogonum wrightii 
##                               TRUE                               TRUE 
##               Eriophyllum ambiguum         Eriophyllum confertiflorum 
##                               TRUE                               TRUE 
##               Eriophyllum wallacei                 Erodium cicutarium 
##                               TRUE                               TRUE 
##                    Erodium texanum             Erythranthe cardinalis 
##                               TRUE                               TRUE 
##             Erythranthe floribunda                Erythranthe guttata 
##                               TRUE                               TRUE 
##               Erythranthe parishii             Eschscholzia androuxii 
##                               TRUE                               TRUE 
##           Eschscholzia californica           Eschscholzia minutiflora 
##                               TRUE                               TRUE 
##           Eschscholzia papastillii              Eschscholzia parishii 
##                               TRUE                               TRUE 
##         Eucrypta chrysanthemifolia                 Eucrypta micrantha 
##                               TRUE                               TRUE 
##               Eulobus californicus               Euphorbia abramsiana 
##                               TRUE                               TRUE 
##                Euphorbia arizonica                 Euphorbia eriantha 
##                               TRUE                               TRUE 
##              Euphorbia melanadenia                Euphorbia micromera 
##                               TRUE                               TRUE 
##             Euphorbia pediculifera                Euphorbia polycarpa 
##                               TRUE                               TRUE 
##                 Euphorbia setiloba                  Eustoma exaltatum 
##                               TRUE                               TRUE 
##                     Fagonia laevis               Fagonia pachyacantha 
##                               TRUE                               TRUE 
##            Ferocactus cylindraceus                  Festuca bromoides 
##                               TRUE                               TRUE 
##                  Festuca octoflora               Fouquieria splendens 
##                               TRUE                               TRUE 
##             Funastrum cynanchoides             Funastrum cynanchoides 
##                               TRUE                               TRUE 
##                Funastrum hirtellum               Galium angustifolium 
##                               TRUE                               TRUE 
##                   Galium stellatum                   Geraea canescens 
##                               TRUE                               TRUE 
##                   Gilia angelensis                     Gilia capitata 
##                               TRUE                               TRUE 
##                   Gilia scopulorum                     Gilia stellata 
##                               TRUE                               TRUE 
##            Gutierrezia californica              Gutierrezia sarothrae 
##                               TRUE                               TRUE 
##                  Helianthus annuus              Helianthus petiolaris 
##                               TRUE                               TRUE 
##          Heliotropium curassavicum             Hesperocallis undulata 
##                               TRUE                               TRUE 
##              Hesperoyucca whipplei                 Hibiscus denudatus 
##                               TRUE                               TRUE 
##                     Hilaria rigida                Hirschfeldia incana 
##                               TRUE                               TRUE 
##         Hoffmannseggia microphylla                    Hordeum murinum 
##                               TRUE                               TRUE 
##               Horsfordia newberryi                     Hulsea vestita 
##                               TRUE                               TRUE 
##                   Ambrosia salsola                      Condea emoryi 
##                               TRUE                               TRUE 
##                  Isocoma acradenia                  Cleomella arborea 
##                               TRUE                               TRUE 
##          Johnstonella angustifolia               Johnstonella costata 
##                               TRUE                               TRUE 
##                Cryptantha racemosa                    Juncus bufonius 
##                               TRUE                               TRUE 
##               Justicia californica           Kallstroemia californica 
##                               TRUE                               TRUE 
##           Keckiella antirrhinoides                   Krameria bicolor 
##                               TRUE                               TRUE 
##                    Krameria erecta                     Krameria grayi 
##                               TRUE                               TRUE 
##             Langloisia setosissima                  Larrea tridentata 
##                               TRUE                               TRUE 
##                Lasthenia coronaria                 Lasthenia gracilis 
##                               TRUE                               TRUE 
##                   Layia glandulosa                 Lepidium fremontii 
##                               TRUE                               TRUE 
##               Lepidium lasiocarpum            Lepidospartum squamatum 
##                               TRUE                               TRUE 
##            Leptosiphon chrysanthus               Leptosiphon lemmonii 
##                               TRUE                               TRUE 
##                Leptosyne bigelovii              Leptosyne californica 
##                               TRUE                               TRUE 
##                      Lilium parryi            Linanthus dianthiflorus 
##                               TRUE                               TRUE 
##                  Linanthus jonesii                Linanthus maculatus 
##                               TRUE                               TRUE 
##               Loeflingia squarrosa              Langloisia matthewsii 
##                               TRUE                               TRUE 
##             Loeseliastrum schottii                   Filago arizonica 
##                               TRUE                               TRUE 
##                    Filago depressa                 Filago californica 
##                               TRUE                               TRUE 
##                    Lotus scoparius                    Lotus strigosus 
##                               TRUE                               TRUE 
##                 Bromus tomentellus                 Lupinus arizonicus 
##                               TRUE                               TRUE 
##                    Lupinus bicolor                  Lupinus concinnus 
##                               TRUE                               TRUE 
##              Lupinus hirsutissimus                  Lupinus shockleyi 
##                               TRUE                               TRUE 
##               Lupinus sparsiflorus                  Lupinus truncatus 
##                               TRUE                               TRUE 
##                  Lycium andersonii                    Lycium brevipes 
##                               TRUE                               TRUE 
##                     Lycium cooperi                   Lycium fremontii 
##                               TRUE                               TRUE 
##                 Lyrocarpa coulteri               Lythrum californicum 
##                               TRUE                               TRUE 
##         Malacothamnus fasciculatus               Malacothrix glabrata 
##                               TRUE                               TRUE 
##             Malacothrix stebbinsii                   Malva parviflora 
##                               TRUE                               TRUE 
##                 Mammillaria dioica                   Marah macrocarpa 
##                               TRUE                               TRUE 
##                      Marina parryi                  Medicago lupulina 
##                               TRUE                               TRUE 
##                Medicago polymorpha                  Melica frutescens 
##                               TRUE                               TRUE 
##                  Melica imperfecta                    Melilotus albus 
##                               TRUE                               TRUE 
##                  Melilotus indicus                  Mentzelia affinis 
##                               TRUE                               TRUE 
##               Mentzelia albicaulis               Mentzelia desertorum 
##                               TRUE                               TRUE 
##             Mentzelia hirsutissima              Mentzelia involucrata 
##                               TRUE                               TRUE 
##                  Mentzelia jonesii        Mesembryanthemum nodiflorum 
##                               TRUE                               TRUE 
##                  Mimetanthe pilosa                 Diplacus bigelovii 
##                               TRUE                               TRUE 
##                   Mirabilis laevis               Mirabilis multiflora 
##                               TRUE                               TRUE 
##                Mirabilis tenuiloba              Mohavea confertiflora 
##                               TRUE                               TRUE 
##              Monoptilon bellioides           Muhlenbergia microsperma 
##                               TRUE                               TRUE 
##                    Muilla maritima                       Nama demissa 
##                               TRUE                               TRUE 
##                       Nama hispida              Nasturtium officinale 
##                               TRUE                               TRUE 
##                Prosopis glandulosa                 Spiranthes odorata 
##                               TRUE                               TRUE 
##           Nemacladus glanduliferus              Nemacladus orientalis 
##                               TRUE                               TRUE 
##               Nemacladus rubescens                  Nemacladus tenuis 
##                               TRUE                               TRUE 
##                Nemophila menziesii              Neogaerrhinum filipes 
##                               TRUE                               TRUE 
##                Nicotiana attenuata              Nicotiana clevelandii 
##                               TRUE                               TRUE 
##                   Nicotiana glauca              Nicotiana obtusifolia 
##                               TRUE                               TRUE 
##             Nicotiana quadrivalvis                   Nolina bigelovii 
##                               TRUE                               TRUE 
##                      Nolina parryi                Oenothera deltoides 
##                               TRUE                               TRUE 
##                    Oenothera elata               Oligomeris linifolia 
##                               TRUE                               TRUE 
##                      Olneya tesota             Oncosiphon piluliferus 
##                               TRUE                               TRUE 
##             Oncosiphon piluliferus                  Opuntia basilaris 
##                               TRUE                               TRUE 
##                Opuntia phaeacantha                   Aphyllon cooperi 
##                               TRUE                               TRUE 
##                    Palafoxia arida                Pappostipa speciosa 
##                               TRUE                               TRUE 
##                 Parietaria hespera               Parkinsonia aculeata 
##                               TRUE                               TRUE 
##                Parkinsonia florida                     Pectis papposa 
##                               TRUE                               TRUE 
##              Pectocarya anisocarpa             Pectocarya heterocarpa 
##                               TRUE                               TRUE 
##                Pectocarya linearis            Pectocarya peninsularis 
##                               TRUE                               TRUE 
##              Pectocarya platycarpa               Pectocarya recurvata 
##                               TRUE                               TRUE 
##                  Pectocarya setosa                  Cenchrus setaceus 
##                               TRUE                               TRUE 
##             Penstemon californicus         Penstemon centranthifolius 
##                               TRUE                               TRUE 
##              Penstemon clevelandii                  Cleomella arborea 
##                               TRUE                               TRUE 
##                    Perityle emoryi                 Petalonyx thurberi 
##                               TRUE                               TRUE 
##              Peucephyllum schottii                 Phacelia crenulata 
##                               TRUE                               TRUE 
##                Phacelia brachyloba              Phacelia campanularia 
##                               TRUE                               TRUE 
##                 Phacelia cicutaria                 Phacelia crenulata 
##                               TRUE                               TRUE 
##                Phacelia cryptantha                   Phacelia distans 
##                               TRUE                               TRUE 
##                  Phacelia ivesiana                     Phacelia minor 
##                               TRUE                               TRUE 
##                  Phacelia neglecta               Phacelia pedicellata 
##                               TRUE                               TRUE 
##               Phacelia ramosissima              Phacelia rotundifolia 
##                               TRUE                               TRUE 
##                     Phalaris minor                 Pholisma arenarium 
##                               TRUE                               TRUE 
##            Pholistoma membranaceum          Phoradendron californicum 
##                               TRUE                               TRUE 
##               Physalis crassifolia                   Physaria tenella 
##                               TRUE                               TRUE 
##                Pilostyles thurberi           Plagiobothrys arizonicus 
##                               TRUE                               TRUE 
##                     Plantago ovata                Plantago patagonica 
##                               TRUE                               TRUE 
##                     Hilaria rigida            Pleurocoronis pluriseta 
##                               TRUE                               TRUE 
##                    Pluchea sericea                        Poa secunda 
##                               TRUE                               TRUE 
##            Polypogon monspeliensis                Porophyllum gracile 
##                               TRUE                               TRUE 
##            Proboscidea altheifolia                Prosopis glandulosa 
##                               TRUE                               TRUE 
##                 Prunus fasciculata                   Prunus fremontii 
##                               TRUE                               TRUE 
##            Psathyrotes ramosissima         Pseudognaphalium biolettii 
##                               TRUE                               TRUE 
##              Pseudoziziphus parryi           Psorothamnus arborescens 
##                               TRUE                               TRUE 
##                Psorothamnus emoryi              Psorothamnus schottii 
##                               TRUE                               TRUE 
##              Psorothamnus spinosus           Pterostegia drymarioides 
##                               TRUE                               TRUE 
##                 Pulicaria paludosa            Rafinesquia californica 
##                               TRUE                               TRUE 
##            Rafinesquia neomexicana                     Rhus aromatica 
##                               TRUE                               TRUE 
##                         Rhus ovata                    Ribes indecorum 
##                               TRUE                               TRUE 
##                       Salix exigua                   Salix gooddingii 
##                               TRUE                               TRUE 
##                    Salix laevigata                  Salsola paulsenii 
##                               TRUE                               TRUE 
##                     Salsola tragus               Saltugilia australis 
##                               TRUE                               TRUE 
##                Saltugilia latimeri                      Salvia apiana 
##                               TRUE                               TRUE 
##                   Salvia carduacea                 Salvia columbariae 
##                              FALSE                               TRUE 
##                Salvia eremostachya                     Salvia greatae 
##                               TRUE                               TRUE 
##                      Salvia vaseyi     Sambucus nigra subsp. caerulea 
##                              FALSE                               TRUE 
##             Funastrum cynanchoides                  Schismus arabicus 
##                               TRUE                               TRUE 
##                  Schismus barbatus           Scrophularia californica 
##                               TRUE                               TRUE 
##               Scutellaria mexicana               Senecio californicus 
##                               TRUE                               TRUE 
##                 Senecio mohavensis                  Senegalia greggii 
##                               TRUE                               TRUE 
##                       Senna armata                Senna artemisioides 
##                               TRUE                               TRUE 
##                      Senna covesii                Sesuvium verrucosum 
##                               TRUE                               TRUE 
##               Sidotheca emarginata               Simmondsia chinensis 
##                               TRUE                               TRUE 
##                    Sisymbrium irio               Sisymbrium orientale 
##                               TRUE                               TRUE 
##                  Solanum douglasii                   Solanum parishii 
##                               TRUE                               TRUE 
##               Solanum umbelliferum                  Solidago velutina 
##                               TRUE                               TRUE 
##                      Sonchus asper                  Sonchus oleraceus 
##                               TRUE                               TRUE 
##                Sphaeralcea ambigua                   Stanleya pinnata 
##                               TRUE                               TRUE 
##              Stemodia durantifolia               Stephanomeria exigua 
##                               TRUE                               TRUE 
##           Stephanomeria pauciflora            Stillingia linearifolia 
##                               TRUE                               TRUE 
##               Stillingia spinulosa                     Stipa capensis 
##                               TRUE                               TRUE 
##                   Stipa hymenoides                Pappostipa speciosa 
##                               TRUE                               TRUE 
##        Streptanthella longirostris        Streptanthella longirostris 
##                               TRUE                               TRUE 
##            Stylocline gnaphaloides                    Tamarix aphylla 
##                               TRUE                               TRUE 
##                Tamarix ramosissima           Tetracoccus fasciculatus 
##                               TRUE                               TRUE 
##                  Thamnosma montana            Caulanthus lasiophyllus 
##                               TRUE                               TRUE 
##            Thymophylla pentachaeta             Thysanocarpus curvipes 
##                               TRUE                               TRUE 
##           Tidestromia oblongifolia           Tidestromia suffruticosa 
##                              FALSE                               TRUE 
##                 Tiquilia canescens                   Tiquilia palmeri 
##                               TRUE                               TRUE 
##                   Tiquilia plicata               Tomostima cuneifolia 
##                               TRUE                               TRUE 
##          Trianthema portulacastrum                Tribulus terrestris 
##                               TRUE                               TRUE 
##              Trichoptilium incisum                 Trixis californica 
##                               TRUE                               TRUE 
##              Tropidocarpum gracile                 Uropappus lindleyi 
##                               TRUE                               TRUE 
##        Veronica anagallis-aquatica              Volutaria tubuliflora 
##                               TRUE                               TRUE 
##                  Xylorhiza cognata                 Xylorhiza orcuttii 
##                               TRUE                               TRUE 
##               Xylorhiza tortifolia                   Yucca schidigera 
##                               TRUE                               TRUE 
##                   Zeltnera venusta              Pseudoziziphus parryi 
##                               TRUE                               TRUE
tr <- tol_induced_subtree(ott_id(resolved_subset)[in_tree])
## 
Progress [--------------------------------] 0/1935 (  0%) ?s
Progress [============================] 1935/1935 (100%)  0s
                                                            
## Warning in collapse_singles(tr, show_progress): Dropping singleton nodes with
## labels: Magnoliopsida ott99252, mrcaott2ott2645, mrcaott2ott35778,
## Mesangiospermae ott5298374, mrcaott2ott10930, mrcaott2ott969, mrcaott2ott62529,
## mrcaott2ott8379, eudicotyledons ott431495, Gunneridae ott853757,
## mrcaott2ott8384, mrcaott2ott1479, mrcaott2ott345, Malpighiales ott429482,
## mrcaott345ott22364, mrcaott345ott18689, mrcaott345ott177705,
## mrcaott345ott38722, mrcaott345ott24237, mrcaott345ott30307, mrcaott345ott26478,
## mrcaott345ott191443, mrcaott345ott485790, Euphorbieae ott520955,
## mrcaott345ott1030065, mrcaott8051ott28703, mrcaott8051ott30309,
## mrcaott33275ott41973, mrcaott33275ott402542, mrcaott33275ott334199,
## mrcaott33275ott33286, Euphorbia sect. Poinsettia ott5147152, Euphorbia subsect.
## Erianthae ott5147154, mrcaott42861ott253647, mrcaott42861ott42866,
## mrcaott42861ott343513, mrcaott42861ott124900, mrcaott376444ott1005185,
## mrcaott42868ott72820, mrcaott716894ott7056399, mrcaott550766ott989270,
## mrcaott30323ott34866, mrcaott504ott36284, mrcaott504ott10167,
## mrcaott10167ott241549, mrcaott10167ott64672, mrcaott10167ott52218,
## mrcaott52218ott764979, mrcaott52218ott262937, Bernardia (genus in kingdom
## Archaeplastida) ott523028, mrcaott30317ott209327, mrcaott30317ott72561,
## mrcaott72561ott147420, mrcaott147420ott610290, mrcaott147420ott230733,
## mrcaott147420ott190669, mrcaott147420ott402227, mrcaott147420ott816389,
## Acalypha ott560972, mrcaott170575ott211956, mrcaott6748ott423256,
## mrcaott6748ott30319, mrcaott6748ott6752, mrcaott6752ott362813,
## mrcaott6752ott174819, mrcaott6752ott671151, mrcaott6752ott6762,
## mrcaott6762ott16262, mrcaott6762ott19547, mrcaott6762ott592498,
## mrcaott6762ott6764, mrcaott6762ott426179, mrcaott6762ott24605,
## mrcaott6762ott16264, mrcaott16264ott16279, mrcaott16264ott426168,
## mrcaott3949ott15752, mrcaott3949ott28711, Picrodendraceae ott62391,
## mrcaott28711ott28714, mrcaott28714ott788306, Tetracoccus (genus in domain
## Eukaryota) ott33336, mrcaott3853ott8858, mrcaott8858ott33097,
## mrcaott8858ott12186, mrcaott8858ott98085, Salicaceae ott530183,
## mrcaott8858ott270454, mrcaott8858ott703490, mrcaott8858ott33085,
## mrcaott8858ott102531, mrcaott8858ott502530, mrcaott8858ott737360,
## mrcaott8858ott474976, Saliceae ott509390, mrcaott86747ott895191,
## mrcaott86747ott531336, mrcaott531336ott725903, mrcaott725903ott738780,
## mrcaott725903ott795555, mrcaott164187ott164212, mrcaott164212ott567279,
## mrcaott567279ott786842, mrcaott567279ott567287, mrcaott567279ott738777,
## mrcaott371ott63303, mrcaott371ott42100, mrcaott371ott22991, Urticaceae
## ott658494, mrcaott22991ott23000, mrcaott22991ott266711, mrcaott22991ott431744,
## mrcaott431744ott723994, mrcaott431744ott472752, Parietaria ott630640,
## mrcaott773ott137975, Rhamnaceae ott329916, Pseudoziziphus ott7056810, Rosaceae
## ott208036, Amygdaloideae ott731134, mrcaott10421ott156934,
## mrcaott156934ott295908, Kerrieae ott901804, mrcaott538527ott817076, Coleogyne
## ott817078, mrcaott34671ott244226, mrcaott61998ott1012886,
## mrcaott61998ott132521, mrcaott61998ott1018655, mrcaott61998ott990519,
## mrcaott61998ott946407, Dryadoideae ott366727, mrcaott122440ott207997,
## mrcaott122440ott653075, mrcaott653075ott7056984, mrcaott2511ott32687,
## mrcaott2511ott253321, mrcaott2511ott29878, Cucurbitaceae ott1006267,
## mrcaott2511ott4028, mrcaott2511ott2972, mrcaott2511ott376422,
## mrcaott2511ott351037, mrcaott2511ott14789, mrcaott2511ott14774,
## mrcaott2511ott182773, mrcaott2511ott185940, mrcaott2511ott132044,
## mrcaott2511ott2520, mrcaott2520ott14778, mrcaott2520ott11772, Cucurbiteae
## ott77740, mrcaott11772ott84409, mrcaott84409ott337509, mrcaott84409ott841310,
## mrcaott84409ott841300, Cucurbita (genus in kingdom Archaeplastida) ott379277,
## Sicyoeae ott462358, mrcaott4000ott103106, mrcaott4000ott67706,
## mrcaott4000ott10298, mrcaott10298ott870455, mrcaott10298ott103086,
## mrcaott103086ott103110, Marah ott1066441, mrcaott198664ott212996, Echinopepon
## ott198658, mrcaott309341ott337493, mrcaott309341ott760212, Apodanthaceae
## ott167651, Pilostyles ott809744, Fabales ott956360, mrcaott579ott179386,
## Fabaceae ott560323, mrcaott579ott730, mrcaott579ott45621, mrcaott579ott8603,
## Papilionoideae ott39538, mrcaott579ott5468, mrcaott579ott5457,
## mrcaott579ott5462, mrcaott579ott5470, mrcaott579ott5091, mrcaott579ott5515,
## mrcaott579ott38037, mrcaott579ott7223, mrcaott579ott11248,
## mrcaott11248ott11254, mrcaott11248ott120275, mrcaott11248ott25572,
## mrcaott11248ott75662, mrcaott11248ott24174, mrcaott11248ott11252,
## mrcaott11248ott192321, mrcaott11248ott24170, mrcaott11248ott11264,
## mrcaott11248ott24172, mrcaott11250ott314143, mrcaott11250ott62867,
## mrcaott11250ott11262, mrcaott11250ott62865, mrcaott11250ott132250,
## mrcaott11250ott11258, mrcaott11258ott752495, mrcaott11258ott532649,
## mrcaott11258ott279712, mrcaott11258ott532657, mrcaott11258ott583880,
## mrcaott363910ott462258, mrcaott462258ott563646, mrcaott462258ott596943,
## mrcaott1749ott496549, mrcaott1749ott222250, mrcaott1749ott27613,
## mrcaott1749ott38031, mrcaott38031ott42707, Medicago ott1086823,
## mrcaott38031ott209352, mrcaott38031ott424990, mrcaott38031ott525750,
## mrcaott38031ott170192, mrcaott38031ott193971, mrcaott38031ott760436,
## mrcaott38031ott193970, mrcaott38032ott646077, mrcaott38032ott374489,
## mrcaott38032ott950610, mrcaott38042ott139477, mrcaott38042ott230316,
## mrcaott38042ott262308, mrcaott38042ott1007989, mrcaott38042ott989938,
## mrcaott38042ott771616, mrcaott368370ott1072867, mrcaott34386ott72192,
## mrcaott34386ott253732, mrcaott34386ott42465, mrcaott42465ott1001097,
## mrcaott449763ott526191, mrcaott449763ott931832, Robinieae ott563850,
## mrcaott37541ott114493, mrcaott37541ott688634, Olneya ott688641,
## mrcaott3942ott82511, dalbergioids sensu lato ott7055847, Amorpheae ott615877,
## mrcaott3942ott763790, mrcaott189642ott334591, Marina ott918581,
## mrcaott189643ott189644, mrcaott189643ott920345, mrcaott240355ott240366,
## mrcaott240366ott1090116, mrcaott240366ott240370, mrcaott341195ott763792,
## mrcaott341195ott763784, mrcaott5473ott26267, mrcaott5473ott590008,
## mrcaott5473ott46797, mrcaott5473ott165471, mrcaott5473ott8026,
## mrcaott8026ott33311, mrcaott8026ott31847, Genisteae ott1090346,
## mrcaott8026ott62394, mrcaott8026ott908606, mrcaott8026ott224618,
## mrcaott8026ott398890, mrcaott8026ott8519, mrcaott8519ott726487, Lupinus
## ott878988, mrcaott8519ott222530, mrcaott8519ott388496, mrcaott8519ott553518,
## mrcaott8519ott857028, mrcaott8519ott222528, mrcaott8519ott282245,
## mrcaott282245ott902823, mrcaott902823ott1065704, mrcaott185311ott539267,
## mrcaott265614ott857024, mrcaott265634ott740409, mrcaott265634ott792139,
## mrcaott265634ott282243, mrcaott282243ott940870, mrcaott2644ott112865,
## mrcaott2644ott30537, mrcaott2644ott86941, mrcaott2644ott333121,
## mrcaott2644ott33732, mrcaott2644ott72925, mrcaott2644ott72932,
## mrcaott72932ott87429, mrcaott87429ott471741, mrcaott87429ott471728,
## mrcaott87429ott471732, Hoffmannseggia ott702632, mrcaott321621ott517678,
## mrcaott321621ott896099, mrcaott896099ott923019, mrcaott21759ott946962,
## mrcaott21759ott170059, mrcaott21759ott124017, Senna ott404633,
## mrcaott21759ott68521, mrcaott21759ott148479, mrcaott21759ott68517,
## mrcaott21759ott148477, mrcaott21759ott147099, mrcaott21759ott326851,
## mrcaott21759ott234461, mrcaott21759ott148490, mrcaott68511ott335063,
## mrcaott68511ott234453, mrcaott234453ott757700, mrcaott757700ott808767,
## mrcaott757700ott757709, mrcaott757700ott908908, mrcaott8605ott87214,
## mrcaott8605ott220379, mrcaott8605ott40823, mrcaott8605ott308458,
## mrcaott8605ott659681, mrcaott8605ott26386, mrcaott8613ott472478,
## mrcaott8613ott66199, mrcaott8613ott66193, mrcaott8613ott981814,
## mrcaott8878ott17129, mrcaott8878ott61940, mrcaott61940ott444652,
## mrcaott444652ott479055, mrcaott39645ott65125, mrcaott39645ott233743,
## mrcaott39645ott471736, mrcaott39645ott39654, mrcaott39654ott39656,
## mrcaott39658ott366575, mrcaott366575ott452957, mrcaott444638ott879743,
## Zygophylloideae ott518751, mrcaott2737ott159002, mrcaott2737ott158973,
## mrcaott2737ott158965, mrcaott2737ott760110, mrcaott2738ott2742, Larreoideae
## ott518759, mrcaott199325ott359651, mrcaott199325ott250015, Larrea ott185819,
## mrcaott250015ott414990, mrcaott87296ott462596, mrcaott87296ott199322,
## Tribuloideae ott518754, mrcaott1091855ott3902318, Krameriaceae ott1074652,
## mrcaott464458ott596333, mrcaott464458ott464459, mrcaott571539ott595139,
## mrcaott595139ott1091
#ape::plot.phylo(tr, cex = 1.5, type = "phylogram") # edges are being a pain...seems the whole tree was pruned...yay

Plotting

ott_ids <- tr[[2]]
ott_ids <- gsub("[^0-9 ]", "", ott_ids)
ott_names <- gsub("\\d+", "", tr[[2]])
ott_names <- gsub("\\_ott", "", ott_names)
ott_names <- gsub("_", " ", ott_names)
tree_df <- data.frame(ott_ids, ott_names)

tree_df <- tree_df %>% 
  rename(speciesName = ott_names)

result_df <- tree_df %>%
  left_join(flowering_data3, by = "speciesName")

trait_df <- result_df

#resolved_subset_m <- merge(resolved_tr_subset, flowering_data3, by.x = "unique_name", by.y = "speciesName")

#trait_df <- merge(tree_df, flowering_data3, by.x = "ott_names", by.y = "speciesName",)
tr # try storing the list into this tree objM
## 
## Phylogenetic tree with 473 tips and 360 internal nodes.
## 
## Tip labels:
##   Euphorbia_eriantha_ott776654, Euphorbia_abramsiana_ott42861, Euphorbia_pediculifera_ott1005185, Euphorbia_arizonica_ott42868, Euphorbia_polycarpa_ott72822, Euphorbia_micromera_ott989270, ...
## Node labels:
##   Spermatophyta ott10218, mrcaott2ott121, mrcaott2ott2441, Pentapetalae ott5316182, mrcaott2ott2464, rosids ott1008296, ...
## 
## Rooted; no branch lengths.
# Sort the merged dataframe based on the order of ott_names in tree_df
trait_df <- trait_df[order(match(trait_df$speciesName, tree_df$speciesName)), ]

trait_df <- select(result_df, ott_ids, speciesName, bloomSpecificity, num_years_condition_satisfied)
trait_df <- trait_df %>% 
  mutate(bloomCol = case_when(
    is.na(bloomSpecificity) ~ "grey", 
    bloomSpecificity == "spring bloomer" ~ "darkgreen", 
    bloomSpecificity == "fall bloomer" ~ "darkred", 
    bloomSpecificity == "opportunistic bloomer" ~ "goldenrod"
    
  ))

#ordered_trait_vector <- trait_df$bloomCol[order(match(trait_df$ott_names, trait_df$ott_names))]

tr$traits <- trait_df$bloomCol

ape::plot.phylo(tr, cex = 1.5, type = "phylogram", tip.color = tr$traits) # edges are being a pain...

How do the phenometrics look?

# trait_df <- trait_df %>% 
#   mutate(phenometric_scope =
#            case_when(
#              num_years_condition_satisfied < 10 ~ "grey",
#              num_years_condition_satisfied >= 10 & num_years_condition_satisfied < 20 ~ "steelblue",
#              num_years_condition_satisfied >= 20~ "purple",
#              TRUE ~ "pink"
#              
#            ))
# 
# ape::plot.phylo(tr, cex = 1.5, type = "phylogram", tip.color = trait_df$phenometric_scope) # edges are being a pain...

Some sample data for the package ape